It is worth noting that using dededuplication does consume a lot of memory.
Deduplication tables consume memory and eventually spill over and consume disk space - this causes extra read and write operations for every block of data on which deduplication is attempted cause more I/O waits. A system with large pools with small memory areas does not perform deduplication well. So, if you run the following command on your pool (pool-ssd in this example) sudo zdb -s pool-ssd ..you see something like the following: pool: pool-ssd state: ONLINE scan: scrub repaired 0B in 0 days 00:31:14 with 0 errors on Wed Sep 2 14:35:52 2020 config: NAME STATE READ WRITE CKSUM pool-ssd ONLINE 0 0 0 mirror-0 ONLINE 0 0 0 ata-INTEL_SSDSC2BW480H6_CVTR608104NW480EGN ONLINE 0 0 0 ata-INTEL_SSDSC2BW480H6_CVTR552500S0480EGN ONLINE 0 0 0 errors: No known data errors dedup: DDT entries 4258028, size 448B on disk, 306B in core bucket allocated referenced ______ ______________________________ ______________________________ refcnt blocks LSIZE PSIZE DSIZE blocks LSIZE PSIZE DSIZE ------ ------ ----- ----- ----- ------ ----- ----- ----- 1 3.63M 464G 226G 226G 3.63M 464G 226G 226G 2 376K 46.1G 24.3G 24.3G 822K 100G 53.2G 53.2G 4 51.3K 5.60G 2.51G 2.51G 240K 26.3G 11.8G 11.8G 8 7.49K 925M 544M 544M 77.9K 9.41G 5.47G 5.47G 16 3.32K 415M 261M 261M 68.8K 8.41G 5.35G 5.35G 32 657 78.7M 62.1M 62.1M 29.3K 3.51G 2.79G 2.79G 64 389 46.2M 42.7M 42.7M 34.0K 4.03G 3.78G 3.78G 128 248 30.1M 29.5M 29.5M 44.8K 5.44G 5.32G 5.32G 256 339 42.1M 40.8M 40.8M 123K 15.4G 14.9G 14.9G 512 374 46.8M 46.1M 46.1M 271K 33.9G 33.5G 33.5G 1K 254 31.8M 31.3M 31.3M 355K 44.4G 43.8G 43.8G 2K 5 640K 513K 513K 12.9K 1.61G 1.20G 1.20G 4K 4 512K 512K 512K 22.7K 2.84G 2.84G 2.84G 8K 8 1M 897K 897K 89.3K 11.2G 10.1G 10.1G 64K 2 256K 6K 6K 226K 28.3G 679M 679M Total 4.06M 517G 254G 254G 5.99M 759G 421G 421G --- Looking at the "dedup: DDT entries 4258028, size 448B on disk, 306B in core" line, we have: 4258028 de-dup entries, each entry used 306 bytes, so that's ~1.2GB of memory for just the de-dup/ table. But it is capped at 1/4 the size of the ARC, so you may find on a small memory system such as a raspberry pi that a lot of the dedup table can't be stored in memory and needs to be on-disk, and this increases the I/O waits. It may be an idea to disable de-dup and see if it helps to resolve your issue on a comparatively slow and memory constrained system such as a raspberry pi when you have large pools ** Changed in: zfs-linux (Ubuntu) Status: New => Incomplete ** Changed in: zfs-linux (Ubuntu) Importance: Undecided => Medium ** Changed in: zfs-linux (Ubuntu) Assignee: (unassigned) => Colin Ian King (colin-king) -- You received this bug notification because you are a member of Kernel Packages, which is subscribed to zfs-linux in Ubuntu. https://bugs.launchpad.net/bugs/1899249 Title: OpenZFS writing stalls, under load Status in zfs-linux package in Ubuntu: Incomplete Bug description: Using a QNAP 4-drive USB enclosure, with a set of SSDs, on a Raspberry Pi 8GB. ZFS deduplication, and LZJB compression is enabled. This issue seems to occur, intermittently, after some time (happens with both SMB access, via Samba, and when interacting with the system, via SSH), and never previously occurred, until a few months ago, and I sometimes have to force a reboot of the system (at the cost of some data loss), in order to use it again. The "dmesg" log reports: [25375.911590] z_wr_iss_h D 0 2161 2 0x00000028 [25375.911606] Call trace: [25375.911627] __switch_to+0x104/0x170 [25375.911639] __schedule+0x30c/0x7c0 [25375.911647] schedule+0x3c/0xb8 [25375.911655] io_schedule+0x20/0x58 [25375.911668] rq_qos_wait+0x100/0x178 [25375.911677] wbt_wait+0xb4/0xf0 [25375.911687] __rq_qos_throttle+0x38/0x50 [25375.911700] blk_mq_make_request+0x128/0x610 [25375.911712] generic_make_request+0xb4/0x2d8 [25375.911722] submit_bio+0x48/0x218 [25375.911960] vdev_disk_io_start+0x670/0x9f8 [zfs] [25375.912181] zio_vdev_io_start+0xdc/0x2b8 [zfs] [25375.912400] zio_nowait+0xd4/0x170 [zfs] [25375.912617] vdev_mirror_io_start+0xa8/0x1b0 [zfs] [25375.912839] zio_vdev_io_start+0x248/0x2b8 [zfs] [25375.913057] zio_execute+0xac/0x110 [zfs] [25375.913096] taskq_thread+0x2f8/0x570 [spl] [25375.913108] kthread+0xfc/0x128 [25375.913119] ret_from_fork+0x10/0x1c [25375.913149] INFO: task txg_sync:2333 blocked for more than 120 seconds. [25375.919916] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25375.926848] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25375.934835] txg_sync D 0 2333 2 0x00000028 [25375.934850] Call trace: [25375.934869] __switch_to+0x104/0x170 [25375.934879] __schedule+0x30c/0x7c0 [25375.934887] schedule+0x3c/0xb8 [25375.934899] schedule_timeout+0x9c/0x190 [25375.934908] io_schedule_timeout+0x28/0x48 [25375.934946] __cv_timedwait_common+0x1a8/0x1f8 [spl] [25375.934982] __cv_timedwait_io+0x3c/0x50 [spl] [25375.935205] zio_wait+0x130/0x2a0 [zfs] [25375.935423] dsl_pool_sync+0x3fc/0x498 [zfs] [25375.935650] spa_sync+0x538/0xe68 [zfs] [25375.935867] txg_sync_thread+0x2c0/0x468 [zfs] [25375.935911] thread_generic_wrapper+0x74/0xa0 [spl] [25375.935924] kthread+0xfc/0x128 [25375.935935] ret_from_fork+0x10/0x1c [25375.936017] INFO: task zbackup:75339 blocked for more than 120 seconds. [25375.942780] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25375.949710] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25375.957702] zbackup D 0 75339 5499 0x00000000 [25375.957716] Call trace: [25375.957732] __switch_to+0x104/0x170 [25375.957742] __schedule+0x30c/0x7c0 [25375.957750] schedule+0x3c/0xb8 [25375.957789] cv_wait_common+0x188/0x1b0 [spl] [25375.957823] __cv_wait+0x30/0x40 [spl] [25375.958045] zil_commit_impl+0x234/0xd30 [zfs] [25375.958263] zil_commit+0x48/0x70 [zfs] [25375.958481] zfs_create+0x544/0x7d0 [zfs] [25375.958698] zpl_create+0xb8/0x178 [zfs] [25375.958711] lookup_open+0x4ec/0x6a8 [25375.958721] do_last+0x260/0x8c0 [25375.958730] path_openat+0x84/0x258 [25375.958739] do_filp_open+0x84/0x108 [25375.958752] do_sys_open+0x180/0x2b0 [25375.958763] __arm64_sys_openat+0x2c/0x38 [25375.958773] el0_svc_common.constprop.0+0x80/0x218 [25375.958781] el0_svc_handler+0x34/0xa0 [25375.958791] el0_svc+0x10/0x2cc [25375.958801] INFO: task zbackup:95187 blocked for more than 120 seconds. [25375.965564] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25375.972492] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25375.980479] zbackup D 0 95187 5499 0x00000000 [25375.980493] Call trace: [25375.980514] __switch_to+0x104/0x170 [25375.980525] __schedule+0x30c/0x7c0 [25375.980536] schedule+0x3c/0xb8 [25375.980578] cv_wait_common+0x188/0x1b0 [spl] [25375.980612] __cv_wait+0x30/0x40 [spl] [25375.980834] zil_commit_impl+0x234/0xd30 [zfs] [25375.981052] zil_commit+0x48/0x70 [zfs] [25375.981280] zfs_write+0xa3c/0xb90 [zfs] [25375.981498] zpl_write_common_iovec+0xac/0x120 [zfs] [25375.981726] zpl_iter_write+0xe4/0x150 [zfs] [25375.981766] new_sync_write+0x100/0x1a8 [25375.981776] __vfs_write+0x74/0x90 [25375.981784] vfs_write+0xe4/0x1c8 [25375.981794] ksys_write+0x78/0x100 [25375.981803] __arm64_sys_write+0x24/0x30 [25375.981813] el0_svc_common.constprop.0+0x80/0x218 [25375.981821] el0_svc_handler+0x34/0xa0 [25375.981830] el0_svc+0x10/0x2cc [25375.981842] INFO: task zbackup:95188 blocked for more than 120 seconds. [25375.988615] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25375.995543] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25376.003532] zbackup D 0 95188 5499 0x00000008 [25376.003545] Call trace: [25376.003561] __switch_to+0x104/0x170 [25376.003571] __schedule+0x30c/0x7c0 [25376.003579] schedule+0x3c/0xb8 [25376.003619] cv_wait_common+0x188/0x1b0 [spl] [25376.003654] __cv_wait+0x30/0x40 [spl] [25376.003875] zil_commit_impl+0x234/0xd30 [zfs] [25376.004092] zil_commit+0x48/0x70 [zfs] [25376.004312] zfs_write+0xa3c/0xb90 [zfs] [25376.004530] zpl_write_common_iovec+0xac/0x120 [zfs] [25376.004748] zpl_iter_write+0xe4/0x150 [zfs] [25376.004759] new_sync_write+0x100/0x1a8 [25376.004768] __vfs_write+0x74/0x90 [25376.004776] vfs_write+0xe4/0x1c8 [25376.004785] ksys_write+0x78/0x100 [25376.004794] __arm64_sys_write+0x24/0x30 [25376.004803] el0_svc_common.constprop.0+0x80/0x218 [25376.004811] el0_svc_handler+0x34/0xa0 [25376.004820] el0_svc+0x10/0x2cc [25376.004917] INFO: task zbackup:95231 blocked for more than 120 seconds. [25376.011678] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25376.018587] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25376.026554] zbackup D 0 95231 5499 0x00000000 [25376.026562] Call trace: [25376.026575] __switch_to+0x104/0x170 [25376.026582] __schedule+0x30c/0x7c0 [25376.026588] schedule+0x3c/0xb8 [25376.026615] cv_wait_common+0x188/0x1b0 [spl] [25376.026636] __cv_wait+0x30/0x40 [spl] [25376.026771] zil_commit_impl+0x234/0xd30 [zfs] [25376.026904] zil_commit+0x48/0x70 [zfs] [25376.027042] zfs_write+0xa3c/0xb90 [zfs] [25376.027174] zpl_write_common_iovec+0xac/0x120 [zfs] [25376.027309] zpl_iter_write+0xe4/0x150 [zfs] [25376.027317] new_sync_write+0x100/0x1a8 [25376.027322] __vfs_write+0x74/0x90 [25376.027332] vfs_write+0xe4/0x1c8 [25376.027338] ksys_write+0x78/0x100 [25376.027344] __arm64_sys_write+0x24/0x30 [25376.027350] el0_svc_common.constprop.0+0x80/0x218 [25376.027355] el0_svc_handler+0x34/0xa0 [25376.027361] el0_svc+0x10/0x2cc [25376.027374] INFO: task z_wr_int:95546 blocked for more than 120 seconds. [25376.034203] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25376.041113] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25376.049080] z_wr_int D 0 95546 2 0x00000028 [25376.049089] Call trace: [25376.049100] __switch_to+0x104/0x170 [25376.049106] __schedule+0x30c/0x7c0 [25376.049111] schedule+0x3c/0xb8 [25376.049116] io_schedule+0x20/0x58 [25376.049123] rq_qos_wait+0x100/0x178 [25376.049129] wbt_wait+0xb4/0xf0 [25376.049135] __rq_qos_throttle+0x38/0x50 [25376.049143] blk_mq_make_request+0x128/0x610 [25376.049150] generic_make_request+0xb4/0x2d8 [25376.049156] submit_bio+0x48/0x218 [25376.049292] vdev_disk_io_start+0x670/0x9f8 [zfs] [25376.049423] zio_vdev_io_start+0xdc/0x2b8 [zfs] [25376.049554] zio_nowait+0xd4/0x170 [zfs] [25376.049693] vdev_queue_io_done+0x1ec/0x2a0 [zfs] [25376.049847] zio_vdev_io_done+0xec/0x220 [zfs] [25376.049986] zio_execute+0xac/0x110 [zfs] [25376.050010] taskq_thread+0x2f8/0x570 [spl] [25376.050025] kthread+0xfc/0x128 [25376.050033] ret_from_fork+0x10/0x1c [25376.050041] INFO: task z_wr_int:95553 blocked for more than 120 seconds. [25376.056873] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25376.063780] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25376.071746] z_wr_int D 0 95553 2 0x00000028 [25376.071754] Call trace: [25376.071764] __switch_to+0x104/0x170 [25376.071770] __schedule+0x30c/0x7c0 [25376.071775] schedule+0x3c/0xb8 [25376.071780] io_schedule+0x20/0x58 [25376.071787] rq_qos_wait+0x100/0x178 [25376.071792] wbt_wait+0xb4/0xf0 [25376.071798] __rq_qos_throttle+0x38/0x50 [25376.071806] blk_mq_make_request+0x128/0x610 [25376.071813] generic_make_request+0xb4/0x2d8 [25376.071819] submit_bio+0x48/0x218 [25376.071955] vdev_disk_io_start+0x670/0x9f8 [zfs] [25376.072086] zio_vdev_io_start+0xdc/0x2b8 [zfs] [25376.072217] zio_nowait+0xd4/0x170 [zfs] [25376.072346] vdev_queue_io_done+0x1ec/0x2a0 [zfs] [25376.072476] zio_vdev_io_done+0xec/0x220 [zfs] [25376.072606] zio_execute+0xac/0x110 [zfs] [25376.072629] taskq_thread+0x2f8/0x570 [spl] [25376.072637] kthread+0xfc/0x128 [25376.072643] ret_from_fork+0x10/0x1c [25496.722315] INFO: task z_wr_iss_h:2161 blocked for more than 241 seconds. [25496.729251] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25496.736195] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25496.744197] z_wr_iss_h D 0 2161 2 0x00000028 [25496.744247] Call trace: [25496.744268] __switch_to+0x104/0x170 [25496.744279] __schedule+0x30c/0x7c0 [25496.744288] schedule+0x3c/0xb8 [25496.744296] io_schedule+0x20/0x58 [25496.744308] rq_qos_wait+0x100/0x178 [25496.744317] wbt_wait+0xb4/0xf0 [25496.744327] __rq_qos_throttle+0x38/0x50 [25496.744340] blk_mq_make_request+0x128/0x610 [25496.744351] generic_make_request+0xb4/0x2d8 [25496.744362] submit_bio+0x48/0x218 [25496.744600] vdev_disk_io_start+0x670/0x9f8 [zfs] [25496.744821] zio_vdev_io_start+0xdc/0x2b8 [zfs] [25496.745039] zio_nowait+0xd4/0x170 [zfs] [25496.745256] vdev_mirror_io_start+0xa8/0x1b0 [zfs] [25496.745473] zio_vdev_io_start+0x248/0x2b8 [zfs] [25496.745690] zio_execute+0xac/0x110 [zfs] [25496.745730] taskq_thread+0x2f8/0x570 [spl] [25496.745742] kthread+0xfc/0x128 [25496.745753] ret_from_fork+0x10/0x1c [25496.745853] INFO: task zbackup:75339 blocked for more than 241 seconds. [25496.752621] Tainted: P C OE 5.4.0-1018-raspi #20-Ubuntu [25496.759557] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. [25496.767547] zbackup D 0 75339 5499 0x00000000 [25496.767561] Call trace: [25496.767585] __switch_to+0x104/0x170 [25496.767595] __schedule+0x30c/0x7c0 [25496.767606] schedule+0x3c/0xb8 [25496.767646] cv_wait_common+0x188/0x1b0 [spl] [25496.767682] __cv_wait+0x30/0x40 [spl] [25496.767906] zil_commit_impl+0x234/0xd30 [zfs] [25496.768126] zil_commit+0x48/0x70 [zfs] [25496.768355] zfs_create+0x544/0x7d0 [zfs] [25496.768574] zpl_create+0xb8/0x178 [zfs] [25496.768595] lookup_open+0x4ec/0x6a8 [25496.768604] do_last+0x260/0x8c0 [25496.768614] path_openat+0x84/0x258 [25496.768624] do_filp_open+0x84/0x108 [25496.768636] do_sys_open+0x180/0x2b0 [25496.768647] __arm64_sys_openat+0x2c/0x38 [25496.768657] el0_svc_common.constprop.0+0x80/0x218 [25496.768665] el0_svc_handler+0x34/0xa0 [25496.768674] el0_svc+0x10/0x2cc tyson@ubuntu:~$ lsb_release -rd Description: Ubuntu 20.04.1 LTS Release: 20.04 tyson@ubuntu:~$ apt-cache policy zfs-dkms zfs-dkms: Installed: 0.8.3-1ubuntu12.4 Candidate: 0.8.3-1ubuntu12.4 Version table: *** 0.8.3-1ubuntu12.4 500 500 http://ports.ubuntu.com/ubuntu-ports focal-updates/universe arm64 Packages 500 http://ports.ubuntu.com/ubuntu-ports focal-updates/universe armhf Packages 100 /var/lib/dpkg/status 0.8.3-1ubuntu12 500 500 http://ports.ubuntu.com/ubuntu-ports focal/universe arm64 Packages 500 http://ports.ubuntu.com/ubuntu-ports focal/universe armhf Packages ProblemType: Bug DistroRelease: Ubuntu 20.04 Package: zfs-dkms 0.8.3-1ubuntu12.4 ProcVersionSignature: Ubuntu 5.4.0-1018.20-raspi 5.4.55 Uname: Linux 5.4.0-1018-raspi aarch64 NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair ApportVersion: 2.20.11-0ubuntu27.8 Architecture: arm64 CasperMD5CheckResult: skip Date: Sat Oct 10 08:50:34 2020 ImageMediaBuild: 20200423.1 PackageArchitecture: all ProcEnviron: TERM=xterm-256color PATH=(custom, no user) XDG_RUNTIME_DIR=<set> LANG=C.UTF-8 SHELL=/bin/bash SourcePackage: zfs-linux UpgradeStatus: No upgrade log present (probably fresh install) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/zfs-linux/+bug/1899249/+subscriptions -- Mailing list: https://launchpad.net/~kernel-packages Post to : kernel-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~kernel-packages More help : https://help.launchpad.net/ListHelp